Again, the 74-76 OMC 9.9/15s were not OMCs best efforts, even though the powerheads and gearcases are very durable. If you are working on this engine for a customer/friend, you might want to limit your exposure to it, or you could end up "being married to it". I’m not saying they can not be made to run satisfactorily, but the learning curve is stiff, especially with the ignition system. Needless to say, if the engine has poor/weak spark, you may be stuck getting involved. But, if both cylinders will jump the 5/16" air gap while cranking, you may not want to get involved further.

The ignition systems can be easily updated to the later CD or "Magflash" style ignition. Should be plenty of them out there from donor engines. I updated a ’74 about a year ago for a fellow that came and did some aluminum work for me. I was impressed by the running quality with the ignition change.

Well, I guess you are into this thing now!
You might luck and just have one bad coil. You could simply swap the coil primary leads to check this theory. If the top cylinder still does not fire with the coils swapped, then you will need to pull that flywheel. If the bottom cylinder refuses to fire with the coils swapped, then you have lucked out and only need a coil. Be sure to check all grounds, and try your spark test with the stop switch leads disconnected also.
As for the shifting problem, I am thinking that someone didn’t get that shift link connector back together properly. The SS screws are easily stripped, and it can be tricky getting that reconnected properly. Make sure the shift rod is properly positioned in the connector, this job is usually easier with an assistant. The other thing to look for is to make sure the lower shift rod (in the gearcase) is threaded all the way down into the gearcase. Once threaded all the way down, simply back it off enough so the top of the shift rod is parallel with the prop shaft and facing forward.
The other suggestion I have is to spread the ears on the brass connector a bit before attempting to reassemble, making it easier for the shift rod to slide into the connector and be properly aligned.
The shift linkage is adjustable between the shift lever and detent as well. But, I don’t think this would be an issue unless someone had messed with this and inadvertently threaded the rod in or out of the plastic block connected to the detent.
I realize that a few pictures would be worth far more than my written words, so feel free to post pictures if you have more questions…Don